The primary function of chemical nomenclature is to ensure that a spoken or written chemical name leaves no ambiguity concerning which chemical compound the name refers to: each chemical name should refer to a single substance. A less important aim is to ensure that each substance has a single name, although a limited number of alternative names is acceptable in some cases.

Preferably, the name also conveys some information about the structure or chemistry of a compound. CAS numbers form an extreme example of names that do not perform this function: each CAS number refers to a single compound but none contain information about the structure.

The form of nomenclature used depends on the audience to which it is addressed. As such, no single correct form exists, but rather there are different forms that are more or less appropriate in different circumstances.

A common name will often suffice to identify a chemical compound in a particular set of circumstances. To be more generally applicable, the name should indicate at least the chemical formula. To be more specific still, the three-dimensional arrangement of the atoms may need to be specified.

In a few specific circumstances (such as the construction of large indices), it becomes necessary to ensure that each compound has a unique name: This requires the addition of extra rules to the standard IUPAC system (the CAS system is the most commonly used in this context), at the expense of having names that are longer and less familiar to most readers. Another system gaining popularity is the International Chemical Identifier (InChI)— which reflects a substance's structure and composition, making it more general than a CAS number.

The IUPAC system is often criticized for the above failures when they become relevant (for example, in differing reactivity of sulfur allotropes, which IUPAC does not distinguish). While IUPAC has a human-readable advantage over CAS numbering, it would be difficult to claim that the IUPAC names for some larger, relevant molecules (such as rapamycin) are human-readable, and so most researchers simply use the informal names.

It is generally understood that the aims of lexicography versus chemical nomenclature vary and are to an extent at odds. Dictionaries of words, whether in traditional print or on the web, collect and report the meanings of words as their uses appear and change over time. For web dictionaries with limited or no formal editorial process, definitions—in this case, definitions of chemical names and terms—can change rapidly without concern for the formal or historical meanings. Chemical nomenclature on the other hand (with IUPAC nomenclature as the best example) is necessarily more restrictive: It aims to standardize communication and practice so that, when a chemical term is used it has a fixed meaning relating to chemical structure, thereby giving insights into chemical properties and derived molecular functions. These differing aims can have profound effects on valid understanding in chemistry, especially with regard to chemical classes that have achieved mass attention. Examples of the impact of these can be seen in considering the examples of:

resveratrol, a single compound clearly defined by this common name, but that can be confused, popularly, with its cis-isomer,

omega-3 fatty acids, a reasonably well-defined chemical structure class that is nevertheless broad as a result of its formal definition, and

polyphenols, a fairly broad structural class with a formal definition, but where mistranslations and general misuse of the term relative to the formal definition has led to serious usage errors, and so ambiguity in the relationship between structure and activity (SAR).

The rapid pace at which meanings can change on the web, in particular for chemical compounds with perceived health benefits, rightly or wrongly ascribed, complicates the matter of maintaining a sound nomenclature (and so access to SAR understanding). A further discussion with specific examples appears in the article on polyphenols, where differing definitions are in use, and there are various, further web definitions and common uses of the word odds with any accepted chemical nomenclature connecting polyphenol structure and bioactivity).

The nomenclature of alchemy is rich in description, but does not effectively meet the aims outlined above. Opinions differ about whether this was deliberate on the part of the early practitioners of alchemy or whether it was a consequence of the particular (and often esoteric) theoretical framework in which they worked.

While both explanations are probably valid to some extent, it is remarkable that the first "modern" system of chemical nomenclature appeared at the same time as the distinction (by Lavoisier) between elements and compounds, in the late eighteenth century.

The recommendations of Guyton covered only what would be today known as inorganic compounds. With the massive expansion of organic chemistry in the mid-nineteenth century and the greater understanding of the structure of organic compounds, the need for a less ad hoc system of nomenclature was felt just as the theoretical tools became available to make this possible. An international conference was convened in Geneva in 1892 by the national chemical societies, from which the first widely accepted proposals for standardization arose.[15]

A commission was set up in 1913 by the Council of the International Association of Chemical Societies, but its work was interrupted by World War I. After the war, the task passed to the newly formed International Union of Pure and Applied Chemistry, which first appointed commissions for organic, inorganic, and biochemical nomenclature in 1921 and continues to do so to this day.

For Type I Ionic Binary Compounds, the cation (a metal in most cases) is named first, and the anion (a nonmetal in most cases) is named second with "-ide" added to it. In these compounds, there is no ambiguity about the oxidation state of an element. The cation takes the name of its elemental form, and the anion name uses the first part of its elemental name with the subsequent addition of the suffix "-ide". For example, the compound LiBr is made up of Li+ cations and Br− anions. Thus, the compound LiBr would be called lithium bromide. The compound BaO, which is composed of Ba2+ cations and O2− anions, is referred to as barium oxide. Note that in these compounds the charges on the ions balance to give a total charge of zero.

Type II Ionic Binary Compounds are those in which the cation does not have a fixed oxidation state – this is very frequent among transition metals. To name these compounds, one must determine the charge of the cation and then write out the name as would be done with Type I Ionic Compounds, except that a Roman numeral (indicating the charge of the cation) is written in parentheses next to the cation name (this is sometimes referred to as Stock nomenclature). For example, take the compound FeCl3. The cation, iron, can occur as Fe2+ and Fe3+. In order for the compound to have a net charge of zero, the cation must be Fe3+ so that the three Cl− anions can be balanced out (3+ and 3− balance to 0). Thus, this compound is called iron(III) chloride. Another example could be the compound PbS2. Because the S2− anion has a subscript of 2 in the formula (giving a 4− charge), the compound must be balanced with a 4+ charge on the Pb cation (lead is a transition metal, and can form cations with a 4+ or a 2+ charge). Thus, the compound is made of one Pb4+ cation to every two S2− anions, the compound is balanced, and its name is written as lead(IV) sulfide. An older system – relying on Latin names for the elements – is also sometimes used to name Type II Ionic Binary Compounds. In this system, the metal (instead of a Roman numeral next to it) has an "-ic" or "-ous" suffix added to it to indicate its oxidation state ("-ous" for lower, "-ic" for higher). For example, the compound FeO contains the Fe2+ cation (which balances out with the O2− anion). Since this oxidation state is lower than the other possibility (Fe3+), this compound is sometimes called ferrous oxide. For the compound, SnO2, the tin ion is Sn4+ (balancing out the 4− charge on the two O2− anions), and because this is a higher oxidation state than the alternative (Sn2+), this compound is called stannic oxide.

Some ionic compounds contain polyatomic ions, which are charged entities containing two or more covalently bonded types of atoms. It is important to know the names of common polyatomic ions; these include ammonium (NH4+), nitrite (NO2−), nitrate (NO3−), sulfite (SO32−), sulfate (SO42−), hydrogen sulfate (bisulfate) (HSO4− ), hydroxide (OH−), cyanide (CN−), phosphate (PO43−), hydrogen phosphate (HPO42−), dihydrogen phosphate (H2PO4−), carbonate (CO32−), hydrogen carbonate (bicarbonate) (HCO3−), hypochlorite (ClO−), chlorite (ClO2−) chlorate (ClO3−), perchlorate (ClO4−), acetate (C2H3O2−), permanganate (MnO4−), dichromate (Cr2O72−) chromate (CrO42−), peroxide (O22−). If you are given the formula Na2SO3, it can be seen that the cation is sodium, or Na+, while the anion is the sulfite ion (SO32−). Therefore, this compound is named sodium sulfite. If the given formula is Ca(OH)2, it can be seen that OH− is the hydroxide ion. Since the charge on the calcium ion is 2+, it makes sense there must be two OH− ions to balance the charge. Therefore, the name of the compound is calcium hydroxide. If one is asked to write the formula for copper(I) chromate, the Roman numeral indicates that copper ion is Cu+ and one can identify that the compound contains the chromate ion (CrO42−). Two of the 1+ copper ions are needed to balance the charge of one 2− chromate ion, so the formula is Cu2CrO4.

Type III Binary Compounds are covalently bonded, an occurrence between nonmetals elements; compounds like these are also known as molecules. In the compound, the first element is named first and with its full elemental name. The second element is named as if it were an anion (root name of the element + "-ide" suffix). Then, prefixes are used to indicate the numbers of each atom present: these prefixes are mono- (one), di- (two), tri- (three), tetra- (four), penta- (five), hexa- (six), hepta- (seven), octa- (eight), nona- (nine), and deca- (ten). The prefix "mono-" is never used with the first element. Thus, NCl3 would be named nitrogen trichloride, P2O5 would be called diphosphorus pentoxide (note how the "a" of the penta- prefix is dropped before the vowel for easier pronunciation), and BF3 would be called boron trifluoride. In the case of being given the name and wishing to write the formula, examples include carbon dioxide, which would be written as CO2, and sulfur tetrafluoride, which is written as SF4. The compounds H2O and NH3, however, are not named according to this system and are referred to by their common names: water and ammonia, respectively.

This naming method generally follows established IUPAC organic nomenclature. Hydrides of the main group elements (groups 13–17) are given -ane base name, e.g. borane (BH3), oxidane (H2O), phosphane (PH3) (Although the name phosphine is also in common use, it is not recommended by IUPAC). The compound PCl3 would thus be named substitutively as trichlorophosphane (with chlorine "substituting"). However, not all such names (or stems) are derived from the element name. For example, NH3 is called "azane" (rather than a word such as nitro-ane which is rather difficult to pronounce in English).

ACD/Name – Generates IUPAC, INDEX (CAS), InChi, Smiles, etc. for drawn structures in 10 languages and translates names to structures. Also available as batch tool and for Pipeline Pilot. Part of I-Lab 2.0